Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population

Lee, Chuen Zhang, Worsley, Sarah F., Davies, Charli S., Komdeur, Jan, Hildebrand, Falk, Dugdale, Hannah L. and Richardson, David S. (2026) Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population. Microbiome. ISSN 2049-2618 (In Press)

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Abstract

Background: The gut microbiome (GM) –important for host health and survival– is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics. Results: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts. Conclusion: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve.

Item Type:	Article
Additional Information:	Availability of data and materials: All 16S sequencing data used in this study can be accessed from European Nucleotide Archive (ENA) database under the study accession numbers PRJEB45408 (samples taken in 2017 and 2018) and PRJEB47095 (samples taken in 2019 and 2020) and PRJEB67634 (samples taken in 2021 and 2022). All shotgun metagenomics data used in this study can be accessed from ENA database under the study accession number PRJEB81709.
Uncontrolled Keywords:	acrocephalus sechellensis,metagenomics,gut microbiome,major histocompatibility complex,wild population
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Organisms and the Environment
Depositing User:	LivePure Connector
Date Deposited:	13 Jan 2026 14:30
Last Modified:	13 Jan 2026 14:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/101594
DOI:	issn:2049-2618

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